From: Nathaniel Eagan (
Date: Mon Jul 01 2013 - 16:21:14 CDT

Hello everyone,

I have created fully-atomistic simulations of a fatty acid in AMBER and
would like to perform a shape-based coarse graining of the molecule
using the built-in CG-builder, but have run into a few snags. I cannot
tell which one is limiting me most, if this application of SBCG is even
possible. Any insight would be appreciated.

I currently have:
AMBER topology files (.top), coordinate files (.crd and original .pdb),
trajectory files (mdcrd), and every other AMBER file associated with
generating a full simulation.

-The CG-builder requires a .psf if I want to keep my generated point charges
     -The .psf generator appears only to work with CHARMM .top or
     -I can find no way to convert AMBER .top to these file types
     -Trying to ignore this and run .psf generator with my .pdb and .top
presents the error that my entire molecule (labeled with a single
residue name) is an unparametrized component---it may just not
understand my topology file format
-The CG-builder seems like it might only be applicable to proteins or
nucleic acids, so a fatty acid may not even work as far as I know

If anyone has any input about how to help or to just flat out tell me
that this will not work, I would greatly appreciate it.

Thank you for your time,